The conformational changes of both partners of a ligand-protein complex, the small-molecule ligand its the protein binding site (in many cases the catalytically active site of an enzyme) are a central aspect many drug actions, as well as a crucial challenge in computational approaches to drug design. In one of the earliest publications in the this field, we showed for a small set of ligands occurring both in the Protein Data Bank (PDB) and the Cambridge Structural Database (CSD) that flexible compounds are not usually bound to a protein in their global vacuum energy conformation, and oftentime not even in any local vacuum energy conformation. While this study used the largest set of data and best methodology available at that time, both the number of structures in either experimental database and the software and hardware resource available have since grown exponentially. We are thus revisiting this important topic with an analysis of orders of magnitudes more structures, and computations performed at a high level of computational quantum-chemical theory. Among other milestones achieved so far in this project, we have extracted all occurrences of small-molecule ligands recently made available in PDB's LigandExpo. As of May 2008, this is a set of over 350,000 distinct sets of 3D coordinates. We have added extensive annotation coming from several different sources. Using these annotations in a chain of filters, we have generated """"""""high-quality"""""""" subsets of ligand structures of high quality and reliability numbering from just about one thousand to about 5,000 occurrences depending on the stringency applied. We have conducted high-level quantum-chemical calculations of conformational energies for these high-quality ligand sets. In the first round, vacuum energy calculations were run partly on our own Linux cluster, partly on the Biowulf cluster of the CIT, NIH. Up to a thousand CPUs were used simultaneously in this computationally massive project, with individual jobs taking from a few hours to several weeks of CPU-time. We obtained results from about 360 runs that completed successfully. These results clearly showed that the possibility for high conformational energies are fully confirmed by these quantum-chemical calculations. They were presented at the eCheminfo 2008 InterAction Meeting at Bryn Mawr, Philadelphia (13-17 October 2008) in the session on PDB Ligands: Analysing their Structure &Binding Data, chaired by Marc Nicklaus. As a result of the discussions about these issues at this session, an international group of """"""""concerned scientists"""""""" has come together, called the Ligand Quality Working Group, which will attempt, in collaborations both informal and more structured, and by free flow of information, to attempt to at least shine a more focused light on this situation, if not improve it in various ways. To explore the possible influence of aqueous environment on ligand conformational energies - after all, vacuum is not really where drug molecules typically operate - a second round of quantum chemical calculations was conducted, employing the SCI-PCM solvent model in Gaussian 03. These runs were even more demanding in terms of computer resources than the vacuum calculations. To analyze the energetic uncertainty as a function of the positional uncertainty, which in turn is a function of the crystallographic resolution, we conducted sampling of conformations with a resolution-dependent torsion distribution centered around the crystal structure conformation at the molecular mechanics force field level. All these results and their discussion and ramifications have been published in a recent major paper (Sitzmann et al., J Chem Inf Model. 52: 739-56, 2012). Related to this topic is a study recently begun on tautomerism of small organic molecules, which is an important question both in chemoinformatics and databases (Project 1), efficient drug design (Projects 2 and 3), and the present project of better understanding protein-ligand interactions and the crystal structures aiding in this quest. This work is mostly being performed by Dr. Laura Guasch-Pamies.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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National Cancer Institute Division of Basic Sciences
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Peach, Megan L; Cachau, Raul E; Nicklaus, Marc C (2017) Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit 30:
Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary et al. (2016) Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure 24:502-508
Guasch, Laura; Sitzmann, Markus; Nicklaus, Marc C (2014) Enumeration of ring-chain tautomers based on SMIRKS rules. J Chem Inf Model 54:2423-32
Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V et al. (2012) PDB ligand conformational energies calculated quantum-mechanically. J Chem Inf Model 52:739-56
Ludek, Olaf R; Schroeder, Gottfried K; Liao, Chenzhong et al. (2009) Synthesis and conformational analysis of locked carbocyclic analogues of 1,3-diazepinone riboside, a high-affinity cytidine deaminase inhibitor. J Org Chem 74:6212-23
Yun, Sang-Moon; Moulaei, Tinoush; Lim, Dan et al. (2009) Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1. Nat Struct Mol Biol 16:876-82
Barchi Jr, Joseph J; Karki, Rajeshri G; Nicklaus, Marc C et al. (2008) Comprehensive structural studies of 2',3'-difluorinated nucleosides: comparison of theory, solution, and solid state. J Am Chem Soc 130:9048-57